commit: 655a8a83559815e73e6e09f6b83fa0905dffee28 Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Sun Oct 2 23:07:43 2016 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Mon Oct 3 20:21:05 2016 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=655a8a83
sci-biology/phrap: Revbump to EAPI=6 Package-Manager: portage-2.3.1 sci-biology/phrap/Manifest | 2 +- .../files/phrap-1.080812-fix-build-system.patch | 100 +++++++++++++++++++++ ...1.080812-r1.ebuild => phrap-1.080812-r2.ebuild} | 16 ++-- 3 files changed, 112 insertions(+), 6 deletions(-) diff --git a/sci-biology/phrap/Manifest b/sci-biology/phrap/Manifest index 1275fda..c3bf6b3 100644 --- a/sci-biology/phrap/Manifest +++ b/sci-biology/phrap/Manifest @@ -1 +1 @@ -DIST phrap-1.080812-distrib.tar.gz 317350 SHA256 7025f3cb30e5a3305a13d150f39a85580ade0bbf8169b25db65cbe396e201052 +DIST phrap-1.080812-distrib.tar.gz 317350 SHA256 7025f3cb30e5a3305a13d150f39a85580ade0bbf8169b25db65cbe396e201052 SHA512 6b125b9a99b6180eb5de16bccfe068abefdb59237fd3295924c418749f2f2d6e39cdbcecc6786e42738846975334c4d8a645eae8fd0fcbda6b0e99241deb15ca WHIRLPOOL e516561804620ba8c96ed0e5c5d791f3fe1e7984e08f646e6fd7c30042f2550f5d1c9b2f800e8a853e42b049b92418ed9d0121e77bf4e9aa895974bce5e73717 diff --git a/sci-biology/phrap/files/phrap-1.080812-fix-build-system.patch b/sci-biology/phrap/files/phrap-1.080812-fix-build-system.patch new file mode 100644 index 00000000..6d30c2c --- /dev/null +++ b/sci-biology/phrap/files/phrap-1.080812-fix-build-system.patch @@ -0,0 +1,100 @@ +* Fix perl shebang to be portable +* Make build system honour LDFLAGS + +--- a/makefile ++++ b/makefile +@@ -25,9 +25,8 @@ + # Makefile for swat, phrap, cross_match, phrapview; also swprobs (currently inactivated) + #CC= icc + #CFLAGS= -O2 -wd266,880 +-CC= cc +-CFLAGS= -O2 +-LFLAGS= -lm ++CC ?= cc ++LIBS = -lm + + SWATOBJS= swat.o weibull.o + +@@ -96,46 +95,46 @@ + chmod a+x phrapview + + swat: makefile $(SWATOBJS) $(SWOBJS) +- $(CC) $(CFLAGS) -o $@ $(SWATOBJS) $(SWOBJS) $(LFLAGS) ++ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ $(SWATOBJS) $(SWOBJS) $(LIBS) + chmod o-r swat + + alpha_swat: makefile $(ALPHOBJS) $(SWOBJS) +- $(CC) $(CFLAGS) -o $@ $(ALPHOBJS) $(SWOBJS) $(LFLAGS) ++ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ $(ALPHOBJS) $(SWOBJS) $(LIBS) + chmod o-r alpha_swat + + swat_counts: makefile $(COUNOBJS) $(SWOBJS) +- $(CC) $(CFLAGS) -o $@ $(COUNOBJS) $(SWOBJS) $(LFLAGS) ++ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ $(COUNOBJS) $(SWOBJS) $(LIBS) + chmod o-r swat_counts + + swprobs: makefile $(PROBOBJS) +- $(CC) $(CFLAGS) -o $@ $(PROBOBJS) $(LFLAGS) ++ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ $(PROBOBJS) $(LIBS) + + phrap: makefile phrap.o call_subs.o $(PHOBJS) $(SCANOBJS) $(SWOBJS) +- $(CC) $(CFLAGS) -o $@ phrap.o call_subs.o $(PHOBJS) $(SCANOBJS) $(SWOBJS) $(LFLAGS) ++ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ phrap.o call_subs.o $(PHOBJS) $(SCANOBJS) $(SWOBJS) $(LIBS) + chmod o-r phrap + + gcphrap: makefile gcphrap.o gccall_subs.o $(PHOBJS) $(SCANOBJS) $(SWOBJS) $(JKBSWOBJS) +- $(CC) $(CFLAGS) -o $@ gcphrap.o gccall_subs.o $(PHOBJS) $(SCANOBJS) $(SWOBJS) $(JKBSWOBJS) $(LFLAGS) ++ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ gcphrap.o gccall_subs.o $(PHOBJS) $(SCANOBJS) $(SWOBJS) $(JKBSWOBJS) $(LIBS) + chmod o-r gcphrap + + cross_match: makefile cross_match.o call_subs.o $(CROBJS) $(SCANOBJS) $(SWOBJS) +- $(CC) $(CFLAGS) -o $@ cross_match.o call_subs.o $(CROBJS) $(SCANOBJS) $(SWOBJS) $(LFLAGS) ++ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ cross_match.o call_subs.o $(CROBJS) $(SCANOBJS) $(SWOBJS) $(LIBS) + chmod o-r cross_match + + gccross_match: makefile gccross_match.o gccall_subs.o $(CROBJS) $(SCANOBJS) $(SWOBJS) $(JKBSWOBJS) +- $(CC) $(CFLAGS) -o $@ gccross_match.o gccall_subs.o $(CROBJS) $(SCANOBJS) $(SWOBJS) $(JKBSWOBJS) $(LFLAGS) ++ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ gccross_match.o gccall_subs.o $(CROBJS) $(SCANOBJS) $(SWOBJS) $(JKBSWOBJS) $(LIBS) + chmod o-r gccross_match + + cluster: makefile $(CLOBJS) call_subs.o $(SCANOBJS) $(SWOBJS) +- $(CC) $(CFLAGS) -o $@ $(CLOBJS) call_subs.o $(SCANOBJS) $(SWOBJS) $(LFLAGS) ++ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ $(CLOBJS) call_subs.o $(SCANOBJS) $(SWOBJS) $(LIBS) + chmod o-r cluster + + loco: makefile $(LOCOOBJS) $(SWOBJS) +- $(CC) $(CFLAGS) -o $@ $(LOCOOBJS) $(SWOBJS) $(LFLAGS) ++ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ $(LOCOOBJS) $(SWOBJS) $(LIBS) + chmod o-r loco + + erf_test: $(ERFOBJS) +- $(CC) $(CFLAGS) -o $@ $(ERFOBJS) $(LFLAGS) ++ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ $(ERFOBJS) $(LIBS) + + loco.o: swat.h + +@@ -228,7 +227,7 @@ + anomalies.o: swat.h + + fast_smith_wat.s: fast_smith_wat.c +- cc -S -machine_code -source_listing -O3 fast_smith_wat.c ++ $(CC) $(CFLAGS) -S -machine_code -source_listing fast_smith_wat.c + #N.B. fast_smith_wat.s MUST BE EDITTED BEFORE USE!!! + + tig_node.o: swat.h +--- a/phrapview ++++ b/phrapview +@@ -1,4 +1,4 @@ +-#!/usr/local/bin/perl -w ++#!/usr/bin/env perl + + + #/***************************************************************************** +@@ -25,6 +25,7 @@ + # + #*****************************************************************************/ + ++use warnings; + use strict; + use Tk; + #phrapview version 0.960731 diff --git a/sci-biology/phrap/phrap-1.080812-r1.ebuild b/sci-biology/phrap/phrap-1.080812-r2.ebuild similarity index 75% rename from sci-biology/phrap/phrap-1.080812-r1.ebuild rename to sci-biology/phrap/phrap-1.080812-r2.ebuild index e3a3f9e..3ae2445 100644 --- a/sci-biology/phrap/phrap-1.080812-r1.ebuild +++ b/sci-biology/phrap/phrap-1.080812-r2.ebuild @@ -2,7 +2,9 @@ # Distributed under the terms of the GNU General Public License v2 # $Id$ -EAPI=5 +EAPI=6 + +inherit toolchain-funcs DESCRIPTION="Shotgun assembly and alignment utilities" HOMEPAGE="http://www.phrap.org/"; @@ -21,6 +23,7 @@ RDEPEND=" S="${WORKDIR}" RESTRICT="fetch" +PATCHES=( "${FILESDIR}/${PN}-1.080812-fix-build-system.patch" ) pkg_nofetch() { einfo "Please visit http://www.phrap.org/phredphrapconsed.html and obtain the file" @@ -28,15 +31,18 @@ pkg_nofetch() { einfo "and put it in ${DISTDIR}" } -src_prepare() { - sed -i 's/CFLAGS=/#CFLAGS=/' makefile || die - sed -i 's|#!/usr/local/bin/perl|#!/usr/bin/env perl|' phrapview || die +src_compile() { + emake CC="$(tc-getCC)" \ + CFLAGS="${CFLAGS}" \ + LDFLAGS="${LDFLAGS}" } src_install() { dobin cross_match loco phrap phrapview swat newbin cluster cluster_phrap - for i in {general,phrap,swat}.doc ; do + + local i + for i in {general,phrap,swat}.doc; do newdoc ${i} ${i}.txt done }
